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1.
Key message
Cork oak has buds protected by the full thickness of its substantial phellem, thus explaining why it is the only European tree that can epicormically resprout after higher intensity fire.Abstract
Epicormic resprouting has various ecological advantages over basal resprouting. However, after higher intensity fires epicormic resprouting is rare as it is difficult for trees and shrubs to keep both their buds and vascular cambia alive. Quercus suber (cork oak) is the only European tree that can resprout epicormically after higher intensity fires. Q. suber develops very thick bark and it has been assumed, without anatomical evidence, that the bark protects the epicormic buds. We investigated if developmental anatomy could explain why Q. suber is an excellent post-fire epicormic resprouter. We examined buds from mature Q. suber trees, macroscopically using a stereo microscope and microscopically using semi-thin microtome sections. Q. suber produced buds in the foliage leaf axils and the bud scale axils. With the commencement of extensive phellem (cork) production the base of the epicormic buds remained at, or just below, the level of the phellogen and thus cork began to bury the buds, although a narrow tube connected each bud to the bark surface. Q. suber epicormic buds became deeply buried in the phellem and would be protected from heat by the full phellem thickness. With its rapid and substantial development of phellem Q. suber had well-protected epicormic buds even in relatively small diameter stems. These results provide the anatomical evidence to show why Q. suber is a noted epicormic resprouter after crown fire.2.
Alexandra Rodríguez Jorge Curiel Yuste Ana Rey Jorge Durán Raúl García-Camacho Antonio Gallardo Fernando Valladares 《Plant and Soil》2017,414(1-2):247-263
Background and aims
The occurrence of drought-induced forest die-off events is projected to increase in the future, but we still lack complete understanding of its impact on plant-soil interactions, soil microbial diversity and function. We investigated the effects of holm oak (Quercus ilex) decline (HOD) on soil microbial community and functioning, and how these effects relate to changes in the herbaceous community.Methods
We selected 30 holm oak trees with different defoliation degrees (healthy, affected and dead) and analyzed soil samples collected under the canopy (holm oak ecotype) and out of the influence (grassland ecotype) of each tree.Results
HOD increased potential nitrogen (N) mineralization and decreased inorganic N concentrations. These results could be partially explained by changes in the herbaceous composition, an increased herbaceous abundance and changes in soil microbial functional diversity and structure, with HOD favoring bacteria against fungi. Moreover, herbaceous abundance and microbial functional diversity of holm oak and grassland ecotypes converged with HOD.Conclusions
Our results show that HOD triggers a cascade effect on plant understory and soil microbial communities, as well as a plant succession (savannization) process, where understory species colonize the gaps left by dead holm oaks, with important implications for ecosystem C and N budgets.3.
Jordane Gavinet Bernard Prévosto Anne Bousquet-Melou Raphaël Gros Elodie Quer Virginie Baldy Catherine Fernandez 《Plant and Soil》2018,430(1-2):59-71
Background & Aims
Oak seedling establishment is difficult and may be partly explained by litter-mediated interactions with neighbors. Litter effects can be physical or chemical and result in positive or negative feedback effects for seedlings. Mediterranean species leaves contain high levels of secondary metabolites which suggest that negative litter effects could be important.Methods
Seedlings of Quercus ilex and Quercus pubescens were grown for two years in pots with natural soil and litter inputs from 6 Mediterranean woody species, artificial litter (only physical effect) or bare soil.Results
Litter types had highly different mass loss (41–80%), which correlated with soil organic C, total N and microbial activity. Litter of Q. pubescens increased soil humidity and oak seedlings aerial biomass. Litters of Cotinus coggygria and Rosmarinus officinalis, containing high quantities of phenolics and terpenes respectively, decomposed fast and led to specific soil microbial catabolic profiles but did not influence oak seedling growth, chemistry or mycorrhization rates.Conclusions
Physical litter effects through improved soil humidity seem to be predominant for oak seedling development. Despite high litter phenolics content, we detected no chemical effects on oak seedlings. Litter traits conferring a higher ability to retain soil moisture in dry periods deserve further attention as they may be critical to explain plant-soil feedbacks in Mediterranean ecosystems.4.
Lili Wei Leixi Cao Yanyan Miao Shuju Wu Shumei Xu Ruisheng Wang Jun Du Aihua Liang Yuejun Fu 《Biotechnology letters》2017,39(8):1129-1139
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Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.7.
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Background
Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.Results
We applied our method to several sets of co-expressed genes and were able to define subsets with enrichment in particular biological processes and specific upstream regulatory motifs.Conclusions
These results show the potential of our technique for functional prediction and regulatory motif identification from microarray data.9.
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Alexey A. Dmitriev Anna V. Kudryavtseva George S. Krasnov Nadezhda V. Koroban Anna S. Speranskaya Anastasia A. Krinitsina Maxim S. Belenikin Anastasiya V. Snezhkina Asiya F. Sadritdinova Natalya V. Kishlyan Tatiana A. Rozhmina Olga Yu. Yurkevich Olga V. Muravenko Nadezhda L. Bolsheva Nataliya V. Melnikova 《BMC plant biology》2016,16(3):237
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Background
Clinical statement alone is not enough to predict the progression of disease. Instead, the gene expression profiles have been widely used to forecast clinical outcomes. Many genes related to survival have been identified, and recently miRNA expression signatures predicting patient survival have been also investigated for several cancers. However, miRNAs and their target genes associated with clinical outcomes have remained largely unexplored.Methods
Here, we demonstrate a survival analysis based on the regulatory relationships of miRNAs and their target genes. The patient survivals for the two major cancers, ovarian cancer and glioblastoma multiforme (GBM), are investigated through the integrated analysis of miRNA-mRNA interaction pairs.Results
We found that there is a larger survival difference between two patient groups with an inversely correlated expression profile of miRNA and mRNA. It supports the idea that signatures of miRNAs and their targets related to cancer progression can be detected via this approach.Conclusions
This integrated analysis can help to discover coordinated expression signatures of miRNAs and their target mRNAs that can be employed for therapeutics in human cancers.19.
Kai Tian Xiangshi Kong Jianguo Gao Yanyan Jia Hong Lin Zaihua He Yanli Ji Zhanlin Bei Xingjun Tian 《Plant and Soil》2018,427(1-2):175-189
Background and aims
Bacterial Non-Specific Acid Phosphatase (NSAP) enzymes are capable of dephosphorylating diverse organic phosphoesters but are rarely studied: their distribution in natural and managed environments is poorly understood. The aim of this study was to generate new insight into the environmental distribution of NSAPs and establish their potential global relevance to cycling of organic phosphorus.Methods
We employed bioinformatic tools to determine NSAP diversity and subcellular localization in microbial genomes; used the corresponding NSAP gene sequences to census metagenomes from diverse ecosystems; studied the effect of long-term land management upon NSAP diversity and abundance.Results
Periplasmic class B NSAPs are poorly represented in marine and terrestrial environments, reflecting their association with enteric and pathogenic bacteria. Periplasmic class A and outer membrane-associated class C NSAPs are cosmopolitan. NSAPs are more abundant in marine than terrestrial ecosystems and class C more abundant than class A genes, except in an acidic peat where class A genes dominate. A clear effect of land management upon gene abundance was identified.Conclusions
NSAP genes are cosmopolitan. Class C genes are more widely distributed: their association with the outer-membrane of cells gives them a clear role in the cycling of organic phosphorus, particularly in soils.20.